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Upadhyay V, Lucas A, Patrick C, Mallela KMG. Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions. Methods 2024; 225:52-61. [PMID: 38492901 DOI: 10.1016/j.ymeth.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024] Open
Abstract
Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Casey Patrick
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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de Campos-Mata L, Trinité B, Modrego A, Tejedor Vaquero S, Pradenas E, Pons-Grífols A, Rodrigo Melero N, Carlero D, Marfil S, Santiago C, Raïch-Regué D, Bueno-Carrasco MT, Tarrés-Freixas F, Abancó F, Urrea V, Izquierdo-Useros N, Riveira-Muñoz E, Ballana E, Pérez M, Vergara-Alert J, Segalés J, Carolis C, Arranz R, Blanco J, Magri G. A monoclonal antibody targeting a large surface of the receptor binding motif shows pan-neutralizing SARS-CoV-2 activity. Nat Commun 2024; 15:1051. [PMID: 38316751 PMCID: PMC10844294 DOI: 10.1038/s41467-024-45171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Here we report the characterization of 17T2, a SARS-CoV-2 pan-neutralizing human monoclonal antibody isolated from a COVID-19 convalescent individual infected during the first pandemic wave. 17T2 is a class 1 VH1-58/κ3-20 antibody, derived from a receptor binding domain (RBD)-specific IgA+ memory B cell, with a broad neutralizing activity against former and new SARS-CoV-2 variants, including XBB.1.16 and BA.2.86 Omicron subvariants. Consistently, 17T2 demonstrates in vivo prophylactic and therapeutic activity against Omicron BA.1.1 infection in K18-hACE2 mice. Cryo-electron microscopy reconstruction shows that 17T2 binds the BA.1 spike with the RBD in "up" position and blocks the receptor binding motif, as other structurally similar antibodies do, including S2E12. Yet, unlike S2E12, 17T2 retains its neutralizing activity against all variants tested, probably due to a larger RBD contact area. These results highlight the impact of small structural antibody changes on neutralizing performance and identify 17T2 as a potential candidate for future clinical interventions.
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Affiliation(s)
- Leire de Campos-Mata
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Andrea Modrego
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Sonia Tejedor Vaquero
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Edwards Pradenas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Anna Pons-Grífols
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Natalia Rodrigo Melero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Diego Carlero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - César Santiago
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Dàlia Raïch-Regué
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | | | - Ferran Tarrés-Freixas
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ferran Abancó
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Mónica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Rocío Arranz
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain.
- CIBERINFEC, ISCIII, Madrid, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain.
| | - Giuliana Magri
- Translational Clinical Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
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Agu CV, Cook RL, Martelly W, Gushgari LR, Mohan M, Takulapalli B. Novel sensor-integrated proteome on chip (SPOC) platform with thousands of folded proteins on a 1.5 sq-cm biosensor chip to enable high-throughput real-time label-free screening for kinetic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.575909. [PMID: 38328216 PMCID: PMC10849568 DOI: 10.1101/2024.01.23.575909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
An automated proteomic platform for producing and screening an array of functional proteins on biosensor surfaces was developed to address the challenges of measuring proteomic interaction kinetics in high throughput (HTP). This technology is termed Sensor-Integrated Proteome On Chip (SPOC®) which involves in-situ cell-free protein expression in nano-liter volume wells (nanowells) directly from rapidly customizable arrays of plasmid DNA, facilitating simultaneous capture-purification of up to 2400 unique full-length folded proteins onto a 1.5 sq-cm surface of a single gold biosensor chip. Arrayed SPOC sensors can then be screened by real-time label-free analysis, including surface plasmon resonance (SPR) to generate kinetic affinity, avidity data. Fluorescent and SPR assays were used to demonstrate zero crosstalk between protein spots. The functionality of the SPOC protein array was validated by antibody binding assay, post-translational modification, mutation-mediated differential binding kinetics, and catalytic activity screening on model SPOC protein arrays containing p53, Src, Jun, Fos, HIST1H3A, and SARS-CoV-2 receptor binding domain (RBD) protein variants of interest, among others. Monoclonal antibodies were found to selectively bind their target proteins on the SPOC array. A commercial anti-RBD antibody was used to demonstrate discriminatory binding to numerous SARS-CoV-2 RBD variants of concern with comprehensive kinetic information. With advantages of HTP, flexibility, low-cost, quick turnaround time, and real-time kinetic affinity profiling, the SPOC proteomic platform addresses the challenges of interrogating protein interactions at scale and can be deployed in various research and clinical applications.
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Affiliation(s)
- Chidozie Victor Agu
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Rebecca L Cook
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - William Martelly
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Lydia R Gushgari
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Mukilan Mohan
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
| | - Bharath Takulapalli
- SPOC Proteomics, Inc. 7201 E Henkel Way Suite 285, Scottsdale AZ 85255, United States
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Hendrickx TCJ, Balcaen KDH, Baert M, Haustraete J, Lambrecht BN. Physicochemical and biological stability of diluted vedolizumab in intravenous infusion bags. Eur J Hosp Pharm 2024:ejhpharm-2023-003844. [PMID: 38212080 DOI: 10.1136/ejhpharm-2023-003844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
INTRODUCTION Intravenous vedolizumab is a widely used monoclonal antibody for outpatients with inflammatory bowel disease. Drug preparation is performed on the day of administration, but is time consuming, causing unnecessary in-hospital patient delay and inefficient logistics for preparation and distribution. Storage of vedolizumab ready-to-administer infusions and distribution via pneumatic air tubes could streamline logistics in the outpatient setting. The aim of this study was to test the shelf life and stability of ready-to-administer intravenous infusion bags containing vedolizumab. METHODS For assessing in-use shelf life, the reconstituted product (300 mg fixed dose) was diluted to a concentration of 1.2 mg/mL in 0.9% NaCl under aseptic conditions, and stored in polyolefin infusion bags at 2-8°C prior to analysis. On replicate samples, we measured concentration, physical and chemical stability using sodium dodecyl sulphate polyacrylamide gel electrophoresis, size exclusion chromatography, and multi-angle laser light scattering, as well as biological activity using a biolayer interferometry assay to study target engagement, and endotoxin content to assess microbiological stability. Stability of ready-to-use vedolizumab was assessed also after transportation via pneumatic tube system. Samples were taken at different time points over an observation period of 30 days on four replicate samples. RESULTS For all parameters assessed, the ready-to-use solution of vedolizumab remained stable over a period of at least 30 days. There were no signs of protein aggregation, chemical instability, or loss of binding of the antibody to the α4β7 integrin target. There was no increase in endotoxin concentration over time. No significant difference was seen in antibody structural stability and protein aggregation between samples before and after transportation via pneumatic tube system. CONCLUSION When prepared under aseptic conditions, dissolved ready-to-administer vedolizumab infusion bags can be stored long term at 2-8°C and transported via pneumatic air tube, without observable loss of antibody stability or binding activity.
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Affiliation(s)
| | - Kevin D H Balcaen
- Protein Synthesis Core, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | | | - Jurgen Haustraete
- Protein Synthesis Core, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory for Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
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Reusch J, Andersen JT, Rant U, Schlothauer T. Insight into the avidity-affinity relationship of the bivalent, pH-dependent interaction between IgG and FcRn. MAbs 2024; 16:2361585. [PMID: 38849969 PMCID: PMC11164218 DOI: 10.1080/19420862.2024.2361585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
Monoclonal antibodies (mAbs) as therapeutics necessitate favorable pharmacokinetic properties, including extended serum half-life, achieved through pH-dependent binding to the neonatal Fc receptor (FcRn). While prior research has mainly investigated IgG-FcRn binding kinetics with a focus on single affinity values, it has been shown that each IgG molecule can engage two FcRn molecules throughout an endosomal pH gradient. As such, we present here a more comprehensive analysis of these interactions with an emphasis on both affinity and avidity by taking advantage of switchSENSE technology, a surface-based biosensor where recombinant FcRn was immobilized via short DNA nanolevers, mimicking the membranous orientation of the receptor. The results revealed insight into the avidity-to-affinity relationship, where assessing binding through a pH gradient ranging from pH 5.8 to 7.4 showed that the half-life extended IgG1-YTE has an affinity inflection point at pH 7.2, reflecting its engineering for improved FcRn binding compared with the wild-type counterpart. Furthermore, IgG1-YTE displayed a pH switch for the avidity enhancement factor at pH 6.2, reflecting strong receptor binding to both sides of the YTE-containing Fc, while avidity was abolished at pH 7.4. When compared with classical surface plasmon resonance (SPR) technology and complementary methods, the use of switchSENSE demonstrated superior capabilities in differentiating affinity from avidity within a single measurement. Thus, the methodology provides reliable kinetic rate parameters for both binding modes and their direct relationship as a function of pH. Also, it deciphers the potential effect of the variable Fab arms on FcRn binding, in which SPR has limitations. Our study offers guidance for how FcRn binding properties can be studied for IgG engineering strategies.
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Affiliation(s)
- Johannes Reusch
- Dynamic Biosensors GmbH, Munich, Germany
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | | | - Tilman Schlothauer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
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Hanaee-Ahvaz H, Cserjan-Puschmann M, Mayer F, Tauer C, Albrecht B, Furtmüller PG, Wiltschi B, Hahn R, Striedner G. Antibody fragments functionalized with non-canonical amino acids preserving structure and functionality - A door opener for new biological and therapeutic applications. Heliyon 2023; 9:e22463. [PMID: 38046162 PMCID: PMC10686840 DOI: 10.1016/j.heliyon.2023.e22463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Functionalization of proteins by incorporating reactive non-canonical amino acids (ncAAs) has been widely applied for numerous biological and therapeutic applications. The requirement not to lose the intrinsic properties of these proteins is often underestimated and not considered. Main purpose of this study was to answer the question whether functionalization via residue-specific incorporation of the ncAA N6-[(2-Azidoethoxy) carbonyl]-l-lysine (Azk) influences the properties of the anti-tumor-necrosis-factor-α-Fab (FTN2). Therefore, FTN2Azk variants with different Azk incorporation sites were designed and amber codon suppression was used for production. The functionalized FTN2Azk variants were efficiently produced in fed-batch like μ-bioreactor cultivations in the periplasm of E. coli displaying correct structure and antigen binding affinities comparable to those of wild-type FTN2. Our FTN2Azk variants with reactive handles for diverse conjugates enable tracking of recombinant protein in the production cell, pharmacological studies and translation into new pharmaceutical applications.
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Affiliation(s)
- Hana Hanaee-Ahvaz
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Biopharma Austria, Process Science, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1121, Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Birgit Wiltschi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
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Harmsen MM, Cornelissen JC, van der Wal FJ, Bergervoet JHW, Koene M. Single-Domain Antibody Multimers for Detection of Botulinum Neurotoxin Serotypes C, D, and Their Mosaics in Endopep-MS. Toxins (Basel) 2023; 15:573. [PMID: 37755999 PMCID: PMC10535107 DOI: 10.3390/toxins15090573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Botulinum neurotoxins (BoNTs) are highly toxic proteins that require high-affinity immunocapture reagents for use in endopeptidase-based assays. Here, 30 novel and 2 earlier published llama single-domain antibodies (VHHs) against the veterinary-relevant BoNT serotypes C and D were yeast-produced. These VHHs recognized 10 independent antigenic sites, and many cross-reacted with the BoNT/DC and CD mosaic variants. As VHHs are highly suitable for genetically linking to increase antigen-binding affinity, 52 VHH multimers were produced and their affinity for BoNT/C, D, DC, and CD was determined. A selection of 15 multimers with high affinity (KD < 0.1 nM) was further shown to be resilient to a high salt wash that is used for samples from complex matrices and bound native BoNTs from culture supernatants as shown by Endopep-MS. High-affinity multimers suitable for further development of a highly sensitive Endopep-MS assay include four multimers that bind both BoNT/D and CD with KD of 14-99 pM, one multimer for BoNT/DC (65 pM) that also binds BoNT/C (75 pM), and seven multimers for BoNT/C (<1-19 pM), six of which also bind BoNT/DC with lower affinity (93-508 pM). In addition to application in diagnostic tests, these VHHs could be used for the development of novel therapeutics for animals or humans.
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Affiliation(s)
- Michiel M. Harmsen
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Jan C. Cornelissen
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Fimme J. van der Wal
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Jan H. W. Bergervoet
- Wageningen Plant Research, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
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Pan X, López Acevedo SN, Cuziol C, De Tavernier E, Fahad AS, Longjam PS, Rao SP, Aguilera-Rodríguez D, Rezé M, Bricault CA, Gutiérrez-González MF, de Souza MO, DiNapoli JM, Vigne E, Shahsavarian MA, DeKosky BJ. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model. Front Immunol 2023; 14:1137069. [PMID: 37346047 PMCID: PMC10280637 DOI: 10.3389/fimmu.2023.1137069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/30/2023] [Indexed: 06/23/2023] Open
Abstract
Molecular characterization of antibody immunity and human antibody discovery is mainly carried out using peripheral memory B cells, and occasionally plasmablasts, that express B cell receptors (BCRs) on their cell surface. Despite the importance of plasma cells (PCs) as the dominant source of circulating antibodies in serum, PCs are rarely utilized because they do not express surface BCRs and cannot be analyzed using antigen-based fluorescence-activated cell sorting. Here, we studied the antibodies encoded by the entire mature B cell populations, including PCs, and compared the antibody repertoires of bone marrow and spleen compartments elicited by immunization in a human immunoglobulin transgenic mouse strain. To circumvent prior technical limitations for analysis of plasma cells, we applied single-cell antibody heavy and light chain gene capture from the entire mature B cell repertoires followed by yeast display functional analysis using a cytokine as a model immunogen. We performed affinity-based sorting of antibody yeast display libraries and large-scale next-generation sequencing analyses to follow antibody lineage performance, with experimental validation of 76 monoclonal antibodies against the cytokine antigen that identified three antibodies with exquisite double-digit picomolar binding affinity. We observed that spleen B cell populations generated higher affinity antibodies compared to bone marrow PCs and that antigen-specific splenic B cells had higher average levels of somatic hypermutation. A degree of clonal overlap was also observed between bone marrow and spleen antibody repertoires, indicating common origins of certain clones across lymphoid compartments. These data demonstrate a new capacity to functionally analyze antigen-specific B cell populations of different lymphoid organs, including PCs, for high-affinity antibody discovery and detailed fundamental studies of antibody immunity.
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Affiliation(s)
- Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sheila N. López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Camille Cuziol
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Ahmed S. Fahad
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Mathilde Rezé
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Matías F. Gutiérrez-González
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
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Hussack G, Rossotti MA, van Faassen H, Murase T, Eugenio L, Schrag JD, Ng KKS, Tanha J. Structure-guided design of a potent Clostridiodes difficile toxin A inhibitor. Front Microbiol 2023; 14:1110541. [PMID: 36778856 PMCID: PMC9909335 DOI: 10.3389/fmicb.2023.1110541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Crystal structures of camelid heavy-chain antibody variable domains (VHHs) bound to fragments of the combined repetitive oligopeptides domain of Clostridiodes difficile toxin A (TcdA) reveal that the C-terminus of VHH A20 was located 30 Å away from the N-terminus of VHH A26. Based on this observation, we generated a biparatopic fusion protein with A20 at the N-terminus, followed by a (GS)6 linker and A26 at the C-terminus. This A20-A26 fusion protein shows an improvement in binding affinity and a dramatic increase in TcdA neutralization potency (>330-fold [IC 50]; ≥2,700-fold [IC 99]) when compared to the unfused A20 and A26 VHHs. A20-A26 also shows much higher binding affinity and neutralization potency when compared to a series of control antibody constructs that include fusions of two A20 VHHs, fusions of two A26 VHHs, a biparatopic fusion with A26 at the N-terminus and A20 at the C-terminus (A26-A20), and actoxumab. In particular, A20-A26 displays a 310-fold (IC 50) to 29,000-fold (IC 99) higher neutralization potency than A26-A20. Size-exclusion chromatography-multiangle light scattering (SEC-MALS) analyses further reveal that A20-A26 binds to TcdA with 1:1 stoichiometry and simultaneous engagement of both A20 and A26 epitopes as expected based on the biparatopic design inspired by the crystal structures of TcdA bound to A20 and A26. In contrast, the control constructs show varied and heterogeneous binding modes. These results highlight the importance of molecular geometric constraints in generating highly potent antibody-based reagents capable of exploiting the simultaneous binding of more than one paratope to an antigen.
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Affiliation(s)
- Greg Hussack
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Martin A. Rossotti
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Tomohiko Murase
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Luiz Eugenio
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Joseph D. Schrag
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Kenneth K.-S. Ng
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada,*Correspondence: Kenneth K.-S. Ng,
| | - Jamshid Tanha
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Jamshid Tanha,
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10
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Orlov AV, Burenin AG, Skirda AM, Nikitin PI. Kinetic Analysis of Prostate-Specific Antigen Interaction with Monoclonal Antibodies for Development of a Magnetic Immunoassay Based on Nontransparent Fiber Structures. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228077. [PMID: 36432177 PMCID: PMC9693269 DOI: 10.3390/molecules27228077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Prostate cancer is the second most common cancer diagnosed in men worldwide. Measuring the prostate-specific antigen (PSA) is regarded as essential during prostate cancer screening. Early diagnosis of this disease relapse after radical prostatectomy requires extremely sensitive methods. This research presents an approach to development of an ultrasensitive magnetic sandwich immunoassay, which demonstrates the limit of PSA detection in human serum of 19 pg/mL at a dynamic range exceeding 3.5 orders of concentration. Such attractive performance stems, inter alia, from the kinetic analysis of monoclonal antibodies (mAbs) against free PSA to select the mAbs exhibiting best kinetic characteristics and specificity. The analysis is carried out with a label-free multiplex spectral-correlation interferometry compatible with inexpensive single-use glass sensor chips. The high sensitivity of developed PSA immunoassay is due to electronic quantification of magnetic nanolabels functionalized by the selected mAbs and three-dimension porous filters used as an extended solid phase. The assay is promising for PSA monitoring after radical prostatectomy. The proposed versatile approach can be applied for the rational design of highly sensitive tests for detection of other analytes in many fields, including in vitro diagnostics, veterinary, food safety, etc.
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Affiliation(s)
- Alexey V. Orlov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia
- Correspondence: (A.V.O.); (P.I.N.)
| | - Alexandr G. Burenin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia
| | - Artemiy M. Skirda
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, 119991 Moscow, Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
- Correspondence: (A.V.O.); (P.I.N.)
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11
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The Generation of Dual-Targeting Fusion Protein PD-L1/CD47 for the Inhibition of Triple-Negative Breast Cancer. Biomedicines 2022; 10:biomedicines10081843. [PMID: 36009390 PMCID: PMC9405206 DOI: 10.3390/biomedicines10081843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive subset of breast cancer with limited therapeutic options. However, its immune evasion mechanisms, characterized by the over-expression of the immune checkpoint molecules PD-L1 and CD47, can be targeted in order to facilitate cancer elimination by cells of innate and adaptive immunity. In this paper, we describe the design, preparation, and evaluation of three novel dual-targeting fusion proteins that were based on the structure frame of prototype IAB (innate and adaptive dependent bispecific fusion protein) and the “Orcutt-type IgG-scFv” molecular model. Three molecules with different spatial conformations were designed to improve antigen–antibody affinity by the addition of Ag–Ab binding sites from the variable region sequences of the anti-PD-L1 monoclonal antibody (mAb) atezolizumab and CV1, a high-affinity receptor of CD47. The results showed that the best-performing among the three proteins designed in this study was protein Pro3; its CV1 N-terminus and Fc domain C-terminus were not sterically hindered. Pro3 was better at boosting T cell proliferation and the engulfment of macrophages than the IAB prototype and, at the same time, retained a level of ADCC activity similar to that of IAB. Through improved design, the novel constructed dual-targeting immunomodulatory protein Pro3 was superior at activating the anti-tumor immune response and has thus shown potential for use in clinical applications.
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12
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Wang W, Thiemann S, Chen Q. Utility of SPR technology in biotherapeutic development: Qualification for intended use. Anal Biochem 2022; 654:114804. [PMID: 35839915 DOI: 10.1016/j.ab.2022.114804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 12/16/2022]
Abstract
Surface plasmon resonance (SPR) analysis provides important binding characteristic information for an antibody to its binding partner, such as binding specificity and affinity (KD). In recent years, SPR has been increasingly used in biosimilar development as part of the comparative analytical similarity assessment. Although there is no systematic study describing how to qualify SPR assays, there are various SPR result types (outputs) that have been used for assay qualification in publicly available regulatory documents. The mixed usage of SPR output can cause confusion and can be misleading when comparing binding attributes among antibody molecules. In this report, using a recombinant huIgG1 (mAb 1) antibody as an example, we performed assay qualification strictly based on the nature of the biomolecular interaction. We recommend that KD should be used as the output of assay qualification when the KD can be measured accurately by SPR. When KD cannot be accurately determined in a SPR setting, sensorgram comparison and Parallel Line Analysis (PLA) can be used to qualify the assay. We emphasize the importance of setting up appropriate SPR assay conditions for target and/or Fc receptor interactions to ensure the assay qualification parameters, such as accuracy and repeatability, to meet the criteria acceptable for regulatory filings. With increasing numbers of biotherapeutics being developed, the methods and guidelines provided here can help to align SPR application between the drug development industry and regulatory authorities which will benefit the scientific communities involved in biotherapeutic drug development.
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Affiliation(s)
- Wei Wang
- Department of Therapeutic Discovery, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
| | - Sandra Thiemann
- Biosimilar Business Unit, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Qing Chen
- Department of Therapeutic Discovery, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
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13
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Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken SE, Ljubetič A, Edman N, Ueda G, Chow CM, Johnson M, Addetia A, Navarro MJ, Panpradist N, Gale M, Freedman BS, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Sci Transl Med 2022; 14:eabn1252. [PMID: 35412328 PMCID: PMC9258422 DOI: 10.1126/scitranslmed.abn1252] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.
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Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lydia B. Green
- Amgen Research, Biologic Discovery, Burnaby, V5A 1V7, BC, Canada
| | | | | | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Invizyne Technologies Inc., Monrovia, CA, 91016, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Laboratory Medicine, University of Wisconsin – Madison, Madison, WI, 53705, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department for Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, SI-1000, Slovenia
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, 98195, USA
- USA Medical Scientist Training Program, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Neolukin Therapeutics Inc., Seattle, WA, 98102, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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14
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Selectivity of mTOR-Phosphatidic Acid Interactions Is Driven by Acyl Chain Structure and Cholesterol. Cells 2021; 11:cells11010119. [PMID: 35011681 PMCID: PMC8750377 DOI: 10.3390/cells11010119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022] Open
Abstract
The need to gain insights into the molecular details of peripheral membrane proteins’ specificity towards phosphatidic acid (PA) is undeniable. The variety of PA species classified in terms of acyl chain length and saturation translates into a complicated, enigmatic network of functional effects that exert a critical influence on cell physiology. As a consequence, numerous studies on the importance of phosphatidic acid in human diseases have been conducted in recent years. One of the key proteins in this context is mTOR, considered to be the most important cellular sensor of essential nutrients while regulating cell proliferation, and which also appears to require PA to build stable and active complexes. Here, we investigated the specific recognition of three physiologically important PA species by the mTOR FRB domain in the presence or absence of cholesterol in targeted membranes. Using a broad range of methods based on model lipid membrane systems, we elucidated how the length and saturation of PA acyl chains influence specific binding of the mTOR FRB domain to the membrane. We also discovered that cholesterol exerts a strong modulatory effect on PA-FRB recognition. Our data provide insight into the molecular details of some physiological effects reported previously and reveal novel mechanisms of fine-tuning the signaling cascades dependent on PA.
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15
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Matharu Z, Bee C, Schwarz F, Chen H, Tomlinson M, Wu G, Rakestraw G, Hornsby M, Drake A, Strop P, Rajpal A, Dollinger G. High-Throughput Surface Plasmon Resonance Biosensors for Identifying Diverse Therapeutic Monoclonal Antibodies. Anal Chem 2021; 93:16474-16480. [PMID: 34854675 DOI: 10.1021/acs.analchem.1c03548] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of antibodies targeting diverse functional epitopes on an antigen is highly crucial for discovering effective therapeutic candidates. Employing a traditional stepwise antibody "screening funnel" as well as prioritizing affinity-based selections over epitope-based selections, result in lead antibody panels lacking epitope diversity. In the present study, we employed an array-based surface plasmon resonance (SPR) platform to perform high-throughput epitope binning analysis on a large number of monoclonal antibodies (mAbs) generated in the early drug discovery process. The mAb panel contained clones from different antibody generation techniques and diverse transgenic mouse strains. The epitope binning results were analyzed in unique ways using various visualizations in the form of dendrograms and network plots, which assisted in determining diversity and redundancy in the mAb sample set. The binning data were further integrated with affinity information to evaluate the performance of seven different transgenic mouse strains. The combination of epitope binning results with binding kinetics and sequence analysis provided an effective and efficient way of selecting high affinity antibodies representing a diverse set of sequence families and epitopes.
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Affiliation(s)
- Zimple Matharu
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Christine Bee
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Frontier Medicines, South San Francisco, California 94080, United States
| | - Flavio Schwarz
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Haibin Chen
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Matthew Tomlinson
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Gabriel Wu
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Ginger Rakestraw
- Bristol Myers Squibb, Cambridge, Massachusetts 02142, United States
| | - Michael Hornsby
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Andrew Drake
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Pavel Strop
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Biologics Discovery, Tallac Therapeutics, Burlingame, California 94010, United States
| | - Arvind Rajpal
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Large Molecule Drug Discovery, Genentech, Inc., South San Francisco, California 94080, United States
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
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16
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Small-Sized Co-Polymers for Targeted Delivery of Multiple Imaging and Therapeutic Agents. NANOMATERIALS 2021; 11:nano11112996. [PMID: 34835760 PMCID: PMC8625475 DOI: 10.3390/nano11112996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022]
Abstract
Research has increasingly focused on the delivery of high, often excessive amounts of drugs, neglecting negative aspects of the carrier's physical preconditions and biocompatibility. Among them, little attention has been paid to "small but beautiful" design of vehicle and multiple cargo to achieve effortless targeted delivery into deep tissue. The design of small biopolymers for deep tissue targeted delivery of multiple imaging agents and therapeutics (mini-nano carriers) emphasizes linear flexible polymer platforms with a hydrodynamic diameter of 4 nm to 10 nm, geometrically favoring dynamic juxtaposition of ligands to host receptors, and economic drug content. Platforms of biodegradable, non-toxic poly(β-l-malic acid) of this size carrying multiple chemically bound, optionally nature-derived or synthetic affinity peptides and drugs for a variety of purposes are described in this review with specific examples. The size, shape, and multiple attachments to membrane sites accelerate vascular escape and fast blood clearance, as well as the increase in medical treatment and contrasts for tissue imaging. High affinity antibodies routinely considered for targeting, such as the brain through the blood-brain barrier (BBB), are replaced by moderate affinity binding peptides (vectors), which penetrate at high influxes not achievable by antibodies.
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17
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Wang Q, Wang T, Zhang R, Yang S, McFarland KS, Chung CY, Jia H, Wang LX, Cipollo JF, Betenbaugh MJ. The interplay of protein engineering and glycoengineering to fine-tune antibody glycosylation and its impact on effector functions. Biotechnol Bioeng 2021; 119:102-117. [PMID: 34647616 DOI: 10.1002/bit.27953] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
The N-glycan pattern of an IgG antibody, attached at a conserved site within the fragment crystallizable (Fc) region, is a critical antibody quality attribute whose structural variability can also impact antibody function. For tailoring the Fc glycoprofile, glycoengineering in cell lines as well as Fc amino acid mutations have been applied. Multiple glycoengineered Chinese hamster ovary cell lines were generated, including defucosylated (FUT8KO), α-2,6-sialylated (ST6KI), and defucosylated α-2,6-sialylated (FUT8KOST6KI), expressing either a wild-type anti-CD20 IgG (WT) or phenylalanine to alanine (F241A) mutant. Matrix-assisted laser desorption ionization-time of flight mass spectrometry characterization of antibody N-glycans revealed that the F241A mutation significantly increased galactosylation and sialylation content and glycan branching. Furthermore, overexpression of recombinant human α-2,6-sialyltransferase resulted in a predominance of α-2,6-sialylation rather than α-2,3-sialylation for both WT and heavily sialylated F241A antibody N-glycans. Interestingly, knocking out α-1,6-fucosyltransferase (FUT8KO), which removed core fucose, lowered the content of N-glycans with terminal Gal and increased levels of terminal GlcNAc and Man5 groups on WT antibody. Further complement-dependent cytotoxicity (CDC) analysis revealed that, regardless of the production cells, WT antibody samples have higher cytotoxic CDC activity with more exposed Gal residues compared to their individual F241A mutants. However, the FUT8KO WT antibody, with a large fraction of bi-GlcNAc structures (G0), displayed the lowest CDC activity of all WT antibody samples. Furthermore, for the F241A mutants, a higher CDC activity was observed for α-2,6- compared to α-2,3-sialylation. Antibody-dependent cellular cytotoxicity (ADCC) analysis revealed that the defucosylated WT and F241A mutants showed enhanced in vitro ADCC performance compared to their fucosylated counterparts, with the defucosylated WT antibodies displaying the highest overall ADCC activity, regardless of sialic acid substitution. Moreover, the FcγRIIIA receptor binding by antibodies did not always correspond directly with ADCC result. This study demonstrates that glycoengineering and protein engineering can both promote and inhibit antibody effector functions and represent practical approaches for varying glycan composition and functionalities during antibody development.
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Affiliation(s)
- Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tiexin Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roushu Zhang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Shuang Yang
- Division of Bacterial, Parasitic and Allergenic Products (DBPAP), Laboratory for Bacterial Polysaccharides, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kevin S McFarland
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cheng-Yu Chung
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hongpeng Jia
- Division of Pediatric Surgery, Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - John F Cipollo
- Division of Bacterial, Parasitic and Allergenic Products (DBPAP), Laboratory for Bacterial Polysaccharides, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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18
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Opdensteinen P, Meyer S, Buyel JF. Nicotiana spp. for the Expression and Purification of Functional IgG3 Antibodies Directed Against the Staphylococcus aureus Alpha Toxin. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.737010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Immunoglobulin subclass IgG1 is bound and neutralized effectively by Staphylococcus aureus protein A, allowing the bacterium to evade the host’s adaptive immune response. In contrast, the IgG3 subclass is not bound by protein A and can be used to treat S. aureus infections, including drug-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA). However, the yields of recombinant IgG3 are generally low because this subclass is prone to degradation, and recovery is hindered by the inability to use protein A as an affinity ligand for antibody purification. Here, we investigated plants (Nicotiana spp.) as an alternative to microbes and mammalian cell cultures for the production of an IgG3 antibody specific for the S. aureus alpha toxin. We targeted recombinant IgG3 to different subcellular compartments and tested different chromatography conditions to improve recovery and purification. Finally, we tested the antigen-binding capacity of the purified antibodies. The highest IgG3 levels in planta (>130 mg kg−1 wet biomass) were achieved by targeting the endoplasmic reticulum or apoplast. Although the purity of IgG3 exceeded 95% following protein G chromatography, product recovery requires further improvement. Importantly, the binding affinity of the purified antibodies was in the nanomolar range and thus comparable to previous studies using murine hybridoma cells as the production system.
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19
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Conrad M, Fechner P, Proll G, Gauglitz G. Comparison of methods for quantitative biomolecular interaction analysis. Anal Bioanal Chem 2021; 414:661-673. [PMID: 34505164 PMCID: PMC8748344 DOI: 10.1007/s00216-021-03623-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022]
Abstract
In order to perform good kinetic experiments, not only the experimental conditions have to be optimized, but the evaluation procedure as well. The focus of this work is the in-depth comparison of different approaches and algorithms to determine kinetic rate constants for biomolecular interaction analysis (BIA). The different algorithms are applied not only to flawless simulated data, but also to real-world measurements. We compare five mathematical approaches for the evaluation of binding curves following pseudo-first-order kinetics with different noise levels. In addition, reflectometric interference spectroscopy (RIfS) measurements of two antibodies are evaluated to determine their binding kinetics. The advantages and disadvantages of the individual approach will be investigated and discussed in detail. In summary, we will raise awareness on how to evaluate and judge results from BIA by using different approaches rather than having to rely on “black box” closed (commercial) software packages.
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Affiliation(s)
- Monika Conrad
- Institute of Physical and Theoretical Chemistry (IPTC), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
| | - Peter Fechner
- Institute of Physical and Theoretical Chemistry (IPTC), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Günther Proll
- Institute of Physical and Theoretical Chemistry (IPTC), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Günter Gauglitz
- Institute of Physical and Theoretical Chemistry (IPTC), Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
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20
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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21
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Klausberger M, Duerkop M, Haslacher H, Wozniak-Knopp G, Cserjan-Puschmann M, Perkmann T, Lingg N, Aguilar PP, Laurent E, De Vos J, Hofner M, Holzer B, Stadler M, Manhart G, Vierlinger K, Egger M, Milchram L, Gludovacz E, Marx N, Köppl C, Tauer C, Beck J, Maresch D, Grünwald-Gruber C, Strobl F, Satzer P, Stadlmayr G, Vavra U, Huber J, Wahrmann M, Eskandary F, Breyer MK, Sieghart D, Quehenberger P, Leitner G, Strassl R, Egger AE, Irsara C, Griesmacher A, Hoermann G, Weiss G, Bellmann-Weiler R, Loeffler-Ragg J, Borth N, Strasser R, Jungbauer A, Hahn R, Mairhofer J, Hartmann B, Binder NB, Striedner G, Mach L, Weinhäusel A, Dieplinger B, Grebien F, Gerner W, Binder CJ, Grabherr R. A comprehensive antigen production and characterisation study for easy-to-implement, specific and quantitative SARS-CoV-2 serotests. EBioMedicine 2021; 67:103348. [PMID: 33906067 PMCID: PMC8099623 DOI: 10.1016/j.ebiom.2021.103348] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Antibody tests are essential tools to investigate humoral immunity following SARS-CoV-2 infection or vaccination. While first-generation antibody tests have primarily provided qualitative results, accurate seroprevalence studies and tracking of antibody levels over time require highly specific, sensitive and quantitative test setups. METHODS We have developed two quantitative, easy-to-implement SARS-CoV-2 antibody tests, based on the spike receptor binding domain and the nucleocapsid protein. Comprehensive evaluation of antigens from several biotechnological platforms enabled the identification of superior antigen designs for reliable serodiagnostic. Cut-off modelling based on unprecedented large and heterogeneous multicentric validation cohorts allowed us to define optimal thresholds for the tests' broad applications in different aspects of clinical use, such as seroprevalence studies and convalescent plasma donor qualification. FINDINGS Both developed serotests individually performed similarly-well as fully-automated CE-marked test systems. Our described sensitivity-improved orthogonal test approach assures highest specificity (99.8%); thereby enabling robust serodiagnosis in low-prevalence settings with simple test formats. The inclusion of a calibrator permits accurate quantitative monitoring of antibody concentrations in samples collected at different time points during the acute and convalescent phase of COVID-19 and disclosed antibody level thresholds that correlate well with robust neutralization of authentic SARS-CoV-2 virus. INTERPRETATION We demonstrate that antigen source and purity strongly impact serotest performance. Comprehensive biotechnology-assisted selection of antigens and in-depth characterisation of the assays allowed us to overcome limitations of simple ELISA-based antibody test formats based on chromometric reporters, to yield comparable assay performance as fully-automated platforms. FUNDING WWTF, Project No. COV20-016; BOKU, LBI/LBG.
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Affiliation(s)
- Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Mark Duerkop
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; Novasign GmbH Vienna, Austria
| | - Helmuth Haslacher
- Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Gordana Wozniak-Knopp
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; CD Laboratory for innovative Immunotherapeutics, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Thomas Perkmann
- Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Nico Lingg
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Patricia Pereira Aguilar
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; BOKU Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences (BOKU),Vienna, Austria
| | - Jelle De Vos
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Manuela Hofner
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Barbara Holzer
- Austrian Agency for Health and Food Safety (AGES), Department for Animal Health, Moedling, Austria
| | - Maria Stadler
- Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Klemens Vierlinger
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Margot Egger
- Department of Laboratory Medicine, Konventhospital Barmherzige Brueder Linz and Ordensklinikum Linz Barmherzige Schwestern, Linz, Austria
| | - Lisa Milchram
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Elisabeth Gludovacz
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Nicolas Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Christoph Köppl
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Christopher Tauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Jürgen Beck
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Maresch
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Clemens Grünwald-Gruber
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | | | - Peter Satzer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Gerhard Stadlmayr
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; CD Laboratory for innovative Immunotherapeutics, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Jasmin Huber
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Markus Wahrmann
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Austria
| | - Farsad Eskandary
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Austria
| | - Marie-Kathrin Breyer
- Department of Respiratory and Critical Care Medicine and Ludwig Boltzmann Institute for Lung Health, Otto Wagner Hospital, Vienna, Austria
| | - Daniela Sieghart
- Division of Rheumatology, Department of Medicine III, Medical University of Vienna, Austria
| | - Peter Quehenberger
- Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Gerda Leitner
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Austria
| | - Robert Strassl
- Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Alexander E Egger
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Christian Irsara
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Andrea Griesmacher
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Gregor Hoermann
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria; MLL Munich Leukemia Laboratory, Munich, Germany
| | - Günter Weiss
- Department of Internal Medicine II, Innsbruck Medical University, Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Innsbruck Medical University, Innsbruck, Austria
| | - Judith Loeffler-Ragg
- Department of Internal Medicine II, Innsbruck Medical University, Innsbruck, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Rainer Hahn
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria
| | | | - Boris Hartmann
- Austrian Agency for Health and Food Safety (AGES), Department for Animal Health, Moedling, Austria
| | - Nikolaus B Binder
- Technoclone Herstellung von Diagnostika und Arzneimitteln GmbH, Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria; Novasign GmbH Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria; enGenes Biotech GmbH, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Andreas Weinhäusel
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Benjamin Dieplinger
- Department of Laboratory Medicine, Konventhospital Barmherzige Brueder Linz and Ordensklinikum Linz Barmherzige Schwestern, Linz, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Wilhelm Gerner
- Institute of Immunology, University of Veterinary Medicine, Vienna, Austria; Christian Doppler Laboratory for an Optimized Prediction of Vaccination Success in Pigs, University of Veterinary Medicine, Vienna, Austria; Present address: The Pirbright Institute, Pirbright, United Kingdom
| | - Christoph J Binder
- Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria.
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 18, 1190 Vienna, Austria.
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22
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Ishii H, Zahra MH, Takayanagi A, Seno M. A Novel Artificially Humanized Anti-Cripto-1 Antibody Suppressing Cancer Cell Growth. Int J Mol Sci 2021; 22:ijms22041709. [PMID: 33567764 PMCID: PMC7915030 DOI: 10.3390/ijms22041709] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
Cripto-1 is a member of the EGF-CFC/FRL1/Cryptic family and is involved in embryonic development and carcinogenesis. We designed a novel anti-Cripto-1 artificial antibody and assessed the recognition to the antigen and the potential to suppress the growth of cancer stem cells. First, single chain antibody clones were isolated by bio-panning with the affinity to recombinant Cripto-1 protein from our original phage-display library. Then, the variable regions of heavy chain VH and light chain VL in each clone were fused to constant regions of heavy chain CH and light chain CL regions respectively. These fused genes were expressed in ExpiCHO-S cells to produce artificial humanized antibodies against Cripto-1. After evaluation of the expression levels, one clone was selected and the anti-Cripto-1 antibody was produced and purified. The purified antibody showed affinity to recombinant Cripto-1 at 1.1 pmol and immunoreactivity to cancer tissues and cell lines. The antibody was available to detect the immunoreactivity in tissue microarrays of malignant tumors as well as in Cripto-1 overexpressing cells. Simultaneously, the antibody exhibited the potential to suppress the growth of human colon cancer derived GEO cells overexpressing Cripto-1 with IC50 at approximately 110 nM. The artificially humanized antibody is proposed to be a good candidate to target cancer cells overexpressing Cripto-1.
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Affiliation(s)
- Hiroko Ishii
- GSP Enterprise, Inc., 1-4-38 12F Minato-machi, Naniwaku, Osaka 556-0017, Japan; (H.I.); (A.T.)
| | - Maram H. Zahra
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan;
| | - Atushi Takayanagi
- GSP Enterprise, Inc., 1-4-38 12F Minato-machi, Naniwaku, Osaka 556-0017, Japan; (H.I.); (A.T.)
| | - Masaharu Seno
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan;
- Correspondence: ; Tel./Fax: +81-86-251-8216
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23
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Knowling S, Clark J, Sjuts H, Abdiche YN. Direct Comparison of Label-Free Biosensor Binding Kinetics Obtained on the Biacore 8K and the Carterra LSA. SLAS DISCOVERY 2020; 25:977-984. [PMID: 32646263 DOI: 10.1177/2472555220934814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Funding pressure on the pharmaceutical industry to deliver new medicines to the market under aggressive timelines has led to a demand for analytical tools with higher detection sensitivity, increased throughput, and automation to speed up research and discovery efforts and converge upon clinically fit leads faster. In the quest for therapeutic antibodies, the early adoption of interaction analysis platforms utilizing surface plasmon resonance (SPR) detection provides insightful molecular-level information about the binding properties of antibody libraries that are key to understanding an antibody's mechanism of action and can guide the library-to-leads triage. Here, we sought to compare the binding kinetics obtained on two state-of-the-art high-throughput SPR platforms in an independent study conducted by unrelated groups located on different continents. We show that when experiments were performed by skilled users adhering to SPR best practices and allowed freedom in their assay design, the two platforms yielded near-identical results, establishing them both as reliable tools in accelerating the characterization of antibody libraries in providing critical information needed to advance leads to the clinic.
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Affiliation(s)
| | | | - Hanno Sjuts
- Biologics Research, Sanofi-Aventis Deutschland GmbH, Frankfurt, Hessen, Germany
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24
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Zheng S, Shen F, Jones B, Fink D, Geist B, Nnane I, Zhou Z, Hall J, Malaviya R, Ort T, Wang W. Characterization of concurrent target suppression by JNJ-61178104, a bispecific antibody against human tumor necrosis factor and interleukin-17A. MAbs 2020; 12:1770018. [PMID: 32544369 PMCID: PMC7531573 DOI: 10.1080/19420862.2020.1770018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tumor necrosis factor (TNF) and interleukin (IL)-17A are pleiotropic cytokines implicated in the pathogenesis of several autoimmune diseases including rheumatoid arthritis (RA) and psoriatic arthritis (PsA). JNJ-61178104 is a novel human anti-TNF and anti-IL-17A monovalent, bispecific antibody that binds to both human TNF and human IL-17A with high affinities and blocks the binding of TNF and IL-17A to their receptors in vitro. JNJ-61178104 also potently neutralizes TNF and IL-17A-mediated downstream effects in multiple cell-based assays. In vivo, treatment with JNJ-61178104 resulted in dose-dependent inhibition of cellular influx in a human IL-17A/TNF-induced murine lung neutrophilia model and the inhibitory effects of JNJ-61178104 were more potent than the treatment with bivalent parental anti-TNF or anti-IL-17A antibodies. JNJ-61178104 was shown to engage its targets, TNF and IL-17A, in systemic circulation measured as drug/target complex formation in normal cynomolgus monkeys (cyno). Surprisingly, quantitative target engagement assessment suggested lower apparent in vivo target-binding affinities for JNJ-61178104 compared to its bivalent parental antibodies, despite their similar in vitro target-binding affinities. The target engagement profiles of JNJ-61178104 in humans were in general agreement with the predicted profiles based on cyno data, suggesting similar differences in the apparent in vivo target-binding affinities. These findings show that in vivo target engagement of monovalent bispecific antibody does not necessarily recapitulate that of the molar-equivalent dose of its bivalent parental antibody. Our results also offer valuable insights into the understanding of the pharmacokinetics/pharmacodynamics and target engagement of other bispecific biologics against dimeric and/or trimeric soluble targets in vivo.
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Affiliation(s)
- Songmao Zheng
- Biologics Development Sciences, Janssen Biotherapeutics, Janssen R&D , Spring House, PA, USA
| | - Fang Shen
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Brian Jones
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Damien Fink
- Biologics Development Sciences, Janssen Biotherapeutics, Janssen R&D , Spring House, PA, USA
| | - Brian Geist
- Biologics Development Sciences, Janssen Biotherapeutics, Janssen R&D , Spring House, PA, USA
| | - Ivo Nnane
- Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Zhao Zhou
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Jeff Hall
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Ravi Malaviya
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Tatiana Ort
- Immunology Discovery, Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
| | - Weirong Wang
- Clinical Pharmacology and Pharmacometrics, Janssen R&D , Spring House, PA, USA
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25
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Van Laethem F, Saba I, Lu J, Bhattacharya A, Tai X, Guinter TI, Engelhardt B, Alag A, Rojano M, Ashe JM, Hanada KI, Yang JC, Sun PD, Singer A. Novel MHC-Independent αβTCRs Specific for CD48, CD102, and CD155 Self-Proteins and Their Selection in the Thymus. Front Immunol 2020; 11:1216. [PMID: 32612609 PMCID: PMC7308553 DOI: 10.3389/fimmu.2020.01216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
MHC-independent αβTCRs (TCRs) recognize conformational epitopes on native self-proteins and arise in mice lacking both MHC and CD4/CD8 coreceptor proteins. Although naturally generated in the thymus, these TCRs resemble re-engineered therapeutic chimeric antigen receptor (CAR) T cells in their specificity for MHC-independent ligands. Here we identify naturally arising MHC-independent TCRs reactive to three native self-proteins (CD48, CD102, and CD155) involved in cell adhesion. We report that naturally arising MHC-independent TCRs require high affinity TCR-ligand engagements in the thymus to signal positive selection and that high affinity positive selection generates a peripheral TCR repertoire with limited diversity and increased self-reactivity. We conclude that the affinity of TCR-ligand engagements required to signal positive selection in the thymus inversely determines the diversity and self-tolerance of the mature TCR repertoire that is selected.
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Affiliation(s)
- François Van Laethem
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Ingrid Saba
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Abhisek Bhattacharya
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Xuguang Tai
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Terry I Guinter
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Britta Engelhardt
- Theodor Kocher Institute, Faculty of Bern, Universität Bern, Bern, Switzerland
| | - Amala Alag
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Mirelle Rojano
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Jennifer M Ashe
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - James C Yang
- Surgery Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Peter D Sun
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
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26
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Stack E, McMurray S, McMurray G, Wade J, Clark M, Young G, Marquette K, Jain S, Kelleher K, Chen T, Lin Q, Bloom L, Lin L, Finlay W, Suzuki R, Cunningham O. In vitro affinity optimization of an anti-BDNF monoclonal antibody translates to improved potency in targeting chronic pain states in vivo. MAbs 2020; 12:1755000. [PMID: 32329655 PMCID: PMC7188400 DOI: 10.1080/19420862.2020.1755000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The role of brain-derived neurotrophic factor (BDNF) signaling in chronic pain has been well documented. Given the important central role of BDNF in long term plasticity and memory, we sought to engineer a high affinity, peripherally-restricted monoclonal antibody against BDNF to modulate pain. BDNF shares 100% sequence homology across human and rodents; thus, we selected chickens as an alternative immune host for initial antibody generation. Here, we describe the affinity optimization of complementarity-determining region-grafted, chicken-derived R3bH01, an anti-BDNF antibody specifically blocking the TrkB receptor interaction. Antibody optimization led to the identification of B30, which has a > 300-fold improvement in affinity based on BIAcore, an 800-fold improvement in potency in a cell-based pERK assay and demonstrates exquisite selectivity over related neurotrophins. Affinity improvements measured in vitro translated to in vivo pharmacological activity, with B30 demonstrating a 30-fold improvement in potency over parental R3bH01 in a peripheral nerve injury model. We further demonstrate that peripheral BDNF plays a role in maintaining the plasticity of sensory neurons following nerve damage, with B30 reversing neuron hyperexcitability associated with heat and mechanical stimuli in a dose-dependent fashion. In summary, our data demonstrate that effective sequestration of BDNF via a high affinity neutralizing antibody has potential utility in modulating the pathophysiological mechanisms that drive chronic pain states.
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Affiliation(s)
| | | | | | - Jason Wade
- Biomedicine Design, Pfizer, Dublin, Ireland.,Biomedicine Design, Pfizer, Cambridge, US
| | | | | | | | | | | | - Ting Chen
- Biomedicine Design, Pfizer, Cambridge, US
| | | | | | - Laura Lin
- Biomedicine Design, Pfizer, Cambridge, US
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27
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Brown ME, Bedinger D, Lilov A, Rathanaswami P, Vásquez M, Durand S, Wallace-Moyer I, Zhong L, Nett JH, Burnina I, Caffry I, Lynaugh H, Sinclair M, Sun T, Bukowski J, Xu Y, Abdiche YN. Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors. PLoS One 2020; 15:e0229206. [PMID: 32134960 PMCID: PMC7058304 DOI: 10.1371/journal.pone.0229206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.
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Affiliation(s)
- Michael E. Brown
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
- * E-mail: (MEB); (YNA)
| | | | - Asparouh Lilov
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | | | - Maximiliano Vásquez
- Department of Computational Biology, Adimab, Palo Alto, CA, United States of America
| | - Stéphanie Durand
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Ian Wallace-Moyer
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Lihui Zhong
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Juergen H. Nett
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Irina Burnina
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Isabelle Caffry
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Heather Lynaugh
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Melanie Sinclair
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Tingwan Sun
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - John Bukowski
- Department of Antibody Discovery, Adimab, Lebanon, NH, United States of America
| | - Yingda Xu
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
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28
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Chou CK, Liu YL, Chen YI, Huang PJ, Tsou PH, Chen CT, Lee HH, Wang YN, Hsu JL, Lee JF, Yankeelov TE, Kameoka J, Yeh HC, Hung MC. Digital Receptor Occupancy Assay in Quantifying On- and Off-Target Binding Affinities of Therapeutic Antibodies. ACS Sens 2020; 5:296-302. [PMID: 32073836 DOI: 10.1021/acssensors.9b01736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While monoclonal antibodies are the fastest-growing class of therapeutic agents, we lack a method that can directly quantify the on- and off-target binding affinities of newly developed therapeutic antibodies in crude cell lysates. As a result, some therapeutic antibody candidates could have a moderate on-target binding affinity but a high off-target binding affinity, which not only gives a reduced efficacy but triggers unwanted side effects. Here, we report a single-molecule counting method that precisely quantifies antibody-bound receptors, free receptors, and unbound antibodies in crude cell lysates, termed digital receptor occupancy assay (DRO). Compared to the traditional flow cytometry-based binding assay, DRO assay enables direct and digital quantification of the three molecular species in solution without the additional antibodies for competitive binding. When characterizing the therapeutic antibody, cetuximab, using DRO assay, we found the on-target binding ratio to be 65% and the binding constant (Kd) to be 2.4 nM, while the off-target binding causes the binding constant to decrease by 0.3 nM. Other than cultured cells, the DRO assay can be performed on tumor mouse xenograft models. Thus, DRO is a simple and highly quantitative method for cell-based antibody binding analysis which can be broadly applied to screen and validate new therapeutic antibodies.
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Affiliation(s)
- Chao-Kai Chou
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Yen-Liang Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan 40402
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yuan-I Chen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Po-Jung Huang
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77840, United States
| | - Pei-Hsiang Tsou
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Chun-Te Chen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jennifer L. Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jin-Fong Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Computational Engineering and Sciences, The University of Texas, Austin, Texas 78712, United States
- Department of Diagnostic Medicine, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jun Kameoka
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77840, United States
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan 40402
- Center for Molecular Medicine, China Medical University, Taichung, Taiwan 40402
- Cancer Biology Program, Graduate School of Biomedical Sciences, The University of Texas Health Sciences Center at Houston, Houston, Texas 77030, United States
- Department of Biotechnology, Asia University, Taichung, Taiwan 41354
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29
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Rational design of small molecule RHOA inhibitors for gastric cancer. THE PHARMACOGENOMICS JOURNAL 2020; 20:601-612. [PMID: 32015453 DOI: 10.1038/s41397-020-0153-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 11/08/2022]
Abstract
Previously, we identified Ras homologous A (RHOA) as a major signaling hub in gastric cancer (GC), the third most common cause of cancer death in the world, prompting us to rationally design an efficacious inhibitor of this oncogenic GTPase. Here, based on that previous work, we extend those computational analyses to further pharmacologically optimize anti-RHOA hydrazide derivatives for greater anti-GC potency. Two of these, JK-136 and JK-139, potently inhibited cell viability and migration/invasion of GC cell lines, and mouse xenografts, diversely expressing RHOA. Moreover, JK-136's binding affinity for RHOA was >140-fold greater than Rhosin, a nonclinical RHOA inhibitor. Network analysis of JK-136/-139 vs. Rhosin treatments indicated downregulation of the sphingosine-1-phosphate, as an emerging cancer metabolic pathway in cell migration and motility. We assert that identifying and targeting oncogenic signaling hubs, such as RHOA, represents an emerging strategy for the design, characterization, and translation of new antineoplastics, against gastric and other cancers.
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30
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Eggenstein E, Richter A, Skerra A. FluoroCalins: engineered lipocalins with novel binding functions fused to a fluorescent protein for applications in biomolecular imaging and detection. Protein Eng Des Sel 2019; 32:289-296. [PMID: 31927584 DOI: 10.1093/protein/gzz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 11/14/2022] Open
Abstract
FluoroCalins represent novel bifunctional protein reagents derived from engineered lipocalins fused to a fluorescent reporter protein, here the enhanced green fluorescent protein (eGFP). We demonstrate the construction, facile bacterial production and broad applicability of FluoroCalins using two Anticalin® molecules directed against the tumor vasculature-associated extra domain B of fibronectin (ED-B) and the vascular endothelial growth factor receptor 3, a marker of tumor and lymphangiogenesis. FluoroCalins were prepared with two different spacers: (i) a short Ser3Ala linker and (ii) a long hydrophilic and conformationally unstructured PASylation® polypeptide comprising 200 Pro, Ala and Ser residues. These FluoroCalins were applied for direct target quantification in enzyme-linked immunosorbent assay as well as target detection by flow cytometry and fluorescence microscopy of live and fixed cells, respectively, demonstrating high specificity and signal-to-noise ratio. Hence, FluoroCalins offer a promising alternative to antibody-based reagents for state of the art fluorescent in vitro detection and biomolecular imaging.
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Affiliation(s)
- Evelyn Eggenstein
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Antonia Richter
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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31
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Gao S, Chen S, Lu Q. Real-Time Profiling of Anti-(Epithelial Cell Adhesion Molecule)-Based Immune Capture from Molecules to Cells Using Multiparameter Surface Plasmon Resonance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1040-1046. [PMID: 30605340 DOI: 10.1021/acs.langmuir.8b03898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Antibodies of epithelial cell-adhesion molecule (anti-EpCAM)-based interfaces have proven to be highly efficient at capturing circulating tumor cells (CTCs). To achieve the bonding of anti-EpCAM to the interface, biotin and streptavidin are used to modify the surface. These processes are critical to subsequent cell-capture efficiencies. However, quantitative research on the interactions between biotin, streptavidin, and biotinylated anti-EpCAM on the interface is lacking. In this work, the thermodynamics and kinetics of biomolecular interactions were determined by using surface plasmon resonance. The equilibrium binding affinities for biotinylated anti-EpCAM to streptavidin and streptavidin to biotin (illustrated by biotin-PEG400-thiol) were found to be 2.75 × 106 and 8.82 × 106 M-1, respectively. Each streptavidin can bind up to 2.30 biotinylated anti-EpCAM under thermodynamic equilibrium. The findings provide useful information to optimize the modification of anti-EpCAM and improve the capture efficiency of CTCs.
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Affiliation(s)
- Su Gao
- School of Chemistry and Chemical Engineering, The State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Shuangshuang Chen
- School of Chemical Science and Engineering , Tong Ji University , Shanghai 200092 , China
| | - Qinghua Lu
- School of Chemistry and Chemical Engineering, The State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , Shanghai 200240 , China
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32
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Structural and In Vitro Functional Comparability Analysis of Altebrel™, a Proposed Etanercept Biosimilar: Focus on Primary Sequence and Glycosylation. Pharmaceuticals (Basel) 2019; 12:ph12010014. [PMID: 30658444 PMCID: PMC6469174 DOI: 10.3390/ph12010014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 02/07/2023] Open
Abstract
The demand for reliable comparability studies of biosimilars grows with their increased market share. These studies focus on physicochemical, structural, functional and clinical properties to ensure that a biosimilar has no significant differences to the originator product and can be released into the market without extensive clinical trials. In the current study, Enbrel® (etanercept, the originator) and Altebrel™ (the proposed biosimilar) underwent direct comparison. “Bottom-up” mass spectrometric analysis was used for primary sequence analysis, evaluation of N/O-glycosylation sites and quantification of methionine oxidation. N/O-glycans were analyzed after permethylation derivatization and the effect of N-glycans on in-vitro functionality of etanercept was assayed. Three enzyme peptide mapping resulted in complete identification of the primary structure. It was confirmed that total ion chromatograms are valuable datasets for the analysis of the primary structure of biodrugs. New N/O-glycan structures were identified and all the N-glycans were quantified. Finally, investigation of the functional properties of N-deglycosylated and non-modified etanercept samples using surface plasmon resonance analysis and in-vitro bioassay showed that N-glycosylation has no significant effect on its in-vitro functionality. Analysis of etanercept and its biosimilar, revealed a high similarity in terms of glycosylation, primary structure and in-vitro functionality.
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33
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Sensitivity and drug tolerance of antidrug antibody assays in relation to positive control characteristics. Bioanalysis 2018; 10:1289-1306. [DOI: 10.4155/bio-2018-0091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: Detection and characterization of antidrug antibodies (ADA) play a key role in understanding the relation of ADA with safety and efficacy. Positive controls (PCs) are used to estimate the sensitivity and assay sensitivity in the presence of drug (drug tolerance) of assays to detect ADA. We investigated a number of factors that may drive sensitivity and drug tolerance. Results: We found no correlation between affinity and sensitivity and sensitivity in the presence of drug in multiple assays with two antibody–drug conjugates. Multiple factors that influenced sensitivity and drug tolerance were observed, yet these had limited overall predictive value for all investigated assay formats, PCs and compounds.Conclusion: Assay sensitivity and drug tolerance as studied here, are likely driven by multiple factors such as cut point confidence level, stoichiometry of PC–drug complexes and presentation of epitopes.
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34
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Fathi F, Rahbarghazi R, Rashidi MR. Label-free biosensors in the field of stem cell biology. Biosens Bioelectron 2018; 101:188-198. [DOI: 10.1016/j.bios.2017.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/13/2017] [Indexed: 01/05/2023]
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35
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Fathi F, Rezabakhsh A, Rahbarghazi R, Rashidi MR. Early-stage detection of VE-cadherin during endothelial differentiation of human mesenchymal stem cells using SPR biosensor. Biosens Bioelectron 2017; 96:358-366. [DOI: 10.1016/j.bios.2017.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 02/08/2023]
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36
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Geuijen KPM, Oppers-Tiemissen C, Egging DF, Simons PJ, Boon L, Schasfoort RBM, Eppink MHM. Rapid screening of IgG quality attributes - effects on Fc receptor binding. FEBS Open Bio 2017; 7:1557-1574. [PMID: 28979843 PMCID: PMC5623700 DOI: 10.1002/2211-5463.12283] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022] Open
Abstract
The interactions of therapeutic antibodies with fragment crystallizable γ (Fcγ) receptors and neonatal Fc receptors (FcRn) are measured in vitro as indicators of antibody functional performance. Antibodies are anchored to immune cells through the Fc tail, and these interactions are important for the efficacy and safety of therapeutic antibodies. High‐throughput binding studies on each of the human Fcγ receptor classes (FcγRI, FcγRIIa, FcγRIIb, FcγRIIIa, and FcγRIIIb) as well as FcRn have been developed and performed with human IgG after stress‐induced modifications to identify potential impact in vivo. Interestingly, we found that asparagine deamidation (D‐N) reduced the binding of IgG to the low‐affinity Fcγ receptors (FcγRIIa, FcγRIIb, FcγRIIIa, and FcγRIIIb), while FcγRI and FcRn binding was not impacted. Deglycosylation completely inhibited binding to all Fcγ receptors, but showed no impact on binding to FcRn. On the other hand, afucosylation only impacted binding to FcγRIIIa and FcγRIIIb. Methionine oxidation at levels below 7%, multiple freeze/thaw cycles and short‐term thermal/shake stress did not influence binding to any of the Fc receptors. The presence of high molecular weight species, or aggregates, disturbed measurements in these binding assays; up to 5% of aggregates in IgG samples changed the binding and kinetics to each of the Fc receptors. Overall, the screening assays described in this manuscript prove that rapid and multiplexed binding assays may be a valuable tool for lead optimization, process development, in‐process controls, and biosimilarity assessment of IgGs during development and manufacturing of therapeutic IgGs.
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Affiliation(s)
- Karin P M Geuijen
- Downstream processing Synthon Biopharmaceuticals BV Nijmegen the Netherlands.,Bioprocess Engineering Wageningen University the Netherlands
| | | | - David F Egging
- Preclinical department Synthon Biopharmaceuticals BV Nijmegenthe Netherlands
| | | | | | - Richard B M Schasfoort
- Medical Cell Biophysics group MIRA institute Faculty of Science and Technology University of Twente Enschede the Netherlands
| | - Michel H M Eppink
- Downstream processing Synthon Biopharmaceuticals BV Nijmegen the Netherlands.,Bioprocess Engineering Wageningen University the Netherlands
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37
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Steinicke F, Oltmann-Norden I, Wätzig H. Long term kinetic measurements revealing precision and general performance of surface plasmon resonance biosensors. Anal Biochem 2017; 530:94-103. [DOI: 10.1016/j.ab.2017.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/16/2017] [Accepted: 05/08/2017] [Indexed: 11/29/2022]
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38
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Singh V, Nerimetla R, Yang M, Krishnan S. Magnetite-Quantum Dot Immunoarray for Plasmon-Coupled-Fluorescence Imaging of Blood Insulin and Glycated Hemoglobin. ACS Sens 2017; 2:909-915. [PMID: 28750536 DOI: 10.1021/acssensors.7b00124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
New microarray chip strategies that are sensitive and selective and that can measure low levels of important biomarkers directly in a blood sample are significant for improving human health by allowing timely diagnosis of an abnormal condition. Herein, we designed an antibody-aptamer immunoarray chip to demonstrate simultaneous measurement of blood insulin and glycated hemoglobin (HbA1c) levels relevant to diabetic and prediabetic disorders using a surface plasmon microarray with validation by fluorescence imaging. To accomplish both surface plasmon and fluorescence imaging on the same sample, we decorated magnetite nanoparticles with quantum dots for covalent immobilization of aptamers for subsequent capture and isolation of the aptamers specific for insulin and HbA1c markers from 20-times diluted whole blood samples. Direct clinically relevant analysis, along with fluorescent imaging of the two markers, was achieved by this new immunoarray platform. The limit of detection was 4 pM for insulin and 1% for HbA1c. Examination of cross-talk using thrombin and platelet-derived growth factor confirmed that the designed immunoarray was highly selective for insulin and HbA1c. Surface plasmon kinetic analysis provided apparent binding constants of 0.24 (±0.08) nM and 37 (±3) μM, respectively, for the binding of insulin and HbA1c onto their surface immobilized monoclonal antibodies. Thus, quantitative imaging of ultralow levels of blood biomarker levels with binding kinetics is uniquely obtained in the designed immunoarray chip. In conclusion, this report demonstrates considerable significance of the developed magnetite-quantum dot-bioconjugate strategy for clinical diagnostics of whole blood biomarkers with characterization of molecular binding interactions.
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Affiliation(s)
- Vini Singh
- Department of Chemistry and ‡Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Rajasekhara Nerimetla
- Department of Chemistry and ‡Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Ming Yang
- Department of Chemistry and ‡Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Sadagopan Krishnan
- Department of Chemistry and ‡Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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39
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Wallner J, Lhota G, Schosserer M, Vorauer-Uhl K. An approach for liposome immobilization using sterically stabilized micelles (SSMs) as a precursor for bio-layer interferometry-based interaction studies. Colloids Surf B Biointerfaces 2017; 154:186-194. [DOI: 10.1016/j.colsurfb.2017.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/23/2017] [Accepted: 03/07/2017] [Indexed: 10/20/2022]
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40
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Nobrega RP, Brown M, Williams C, Sumner C, Estep P, Caffry I, Yu Y, Lynaugh H, Burnina I, Lilov A, Desroches J, Bukowski J, Sun T, Belk JP, Johnson K, Xu Y. Database-Centric Method for Automated High-Throughput Deconvolution and Analysis of Kinetic Antibody Screening Data. SLAS Technol 2017; 22:547-556. [PMID: 28430560 DOI: 10.1177/2472630317705611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The state-of-the-art industrial drug discovery approach is the empirical interrogation of a library of drug candidates against a target molecule. The advantage of high-throughput kinetic measurements over equilibrium assessments is the ability to measure each of the kinetic components of binding affinity. Although high-throughput capabilities have improved with advances in instrument hardware, three bottlenecks in data processing remain: (1) intrinsic molecular properties that lead to poor biophysical quality in vitro are not accounted for in commercially available analysis models, (2) processing data through a user interface is time-consuming and not amenable to parallelized data collection, and (3) a commercial solution that includes historical kinetic data in the analysis of kinetic competition data does not exist. Herein, we describe a generally applicable method for the automated analysis, storage, and retrieval of kinetic binding data. This analysis can deconvolve poor quality data on-the-fly and store and organize historical data in a queryable format for use in future analyses. Such database-centric strategies afford greater insight into the molecular mechanisms of kinetic competition, allowing for the rapid identification of allosteric effectors and the presentation of kinetic competition data in absolute terms of percent bound to antigen on the biosensor.
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Affiliation(s)
- R Paul Nobrega
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Michael Brown
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Cody Williams
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Chris Sumner
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Patricia Estep
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Isabelle Caffry
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Yao Yu
- 2 Merck Research Laboratories, Palo Alto, CA, USA
| | - Heather Lynaugh
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Irina Burnina
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Asparouh Lilov
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Jordan Desroches
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - John Bukowski
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Tingwan Sun
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Jonathan P Belk
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Kirt Johnson
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
| | - Yingda Xu
- 1 Adimab LLC, Protein Analytics, Product Engineering, Antibody Discovery, Lebanon, NH, USA
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41
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Yang D, Singh A, Wu H, Kroe-Barrett R. Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms. J Vis Exp 2017. [PMID: 28448040 PMCID: PMC5564993 DOI: 10.3791/55659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.
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Affiliation(s)
- Danlin Yang
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Ajit Singh
- The Fu Foundation School of Engineering and Applied Science, Columbia University
| | - Helen Wu
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Rachel Kroe-Barrett
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc.;
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42
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Kumar R, Jangir DK, Verma G, Shekhar S, Hanpude P, Kumar S, Kumari R, Singh N, Sarovar Bhavesh N, Ranjan Jana N, Kanti Maiti T. S-nitrosylation of UCHL1 induces its structural instability and promotes α-synuclein aggregation. Sci Rep 2017; 7:44558. [PMID: 28300150 PMCID: PMC5353675 DOI: 10.1038/srep44558] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/09/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquitin C-terminal Hydrolase-1 (UCHL1) is a deubiquitinating enzyme, which plays a key role in Parkinson’s disease (PD). It is one of the most important proteins, which constitute Lewy body in PD patient. However, how this well folded highly soluble protein presents in this proteinaceous aggregate is still unclear. We report here that UCHL1 undergoes S-nitrosylation in vitro and rotenone induced PD mouse model. The preferential nitrosylation in the Cys 90, Cys 152 and Cys 220 has been observed which alters the catalytic activity and structural stability. We show here that nitrosylation induces structural instability and produces amorphous aggregate, which provides a nucleation to the native α-synuclein for faster aggregation. Our findings provide a new link between UCHL1-nitrosylation and PD pathology.
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Affiliation(s)
- Roshan Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India.,Manipal University, Manipal, Karnataka, 576104, India
| | - Deepak K Jangir
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India
| | - Garima Verma
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shashi Shekhar
- Molecular Neuroscience Laboratory, National Brain Research Centre (NBRC), Manesar, Gurgaon, 122051, India
| | - Pranita Hanpude
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India.,Manipal University, Manipal, Karnataka, 576104, India
| | - Sanjay Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India.,Manipal University, Manipal, Karnataka, 576104, India
| | - Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India
| | - Nirpendra Singh
- Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nihar Ranjan Jana
- Molecular Neuroscience Laboratory, National Brain Research Centre (NBRC), Manesar, Gurgaon, 122051, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad, 121001, India
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43
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Wang X, Li Z, Ly N, Zhou F. One-Step Ligand Immobilization and Single Sample Injection for Regeneration-Free Surface Plasmon Resonance Measurements of Biomolecular Interactions. Anal Chem 2017; 89:3261-3265. [PMID: 28225259 DOI: 10.1021/acs.analchem.7b00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) has been well established as a method of choice for label-free kinetic measurements of biomolecular interactions. The conventional approach involves multiple injections of an analyte of different concentrations into a fluidic channel covered with a fixed ligand density. Optimization of the experimental conditions and assessment of the data quality can be complicated by issues such as disruption of the ligand structure by the regeneration step and the limited availability of the sample solution. By sequentially closing fluidic channels on a five-channel SPR instrument, different densities of a ligand can be immobilized and determined in one step. With a subsequent injection of a single sample solution, SPR sensorgrams can be simultaneously collected to yield binding and dissociation rate constants (ka and kd) and dissociation constant (KD) between the ligand and analyte. For biomolecular interactions that obey the Langmuir isotherm, we show that the fidelity of the kinetic data can only be reliably confirmed when there exists a strong linear correlation between the SPR signals and the ligand densities. The use of a multichannel SPR instrument also obviates the regeneration step, allowing the binding kinetics between the green fluorescent protein and its antibody to be measured. In comparison to the conventional approach, the method simplifies the experimental procedure, reduces costs associated with sensor chips and biological samples, expedites kinetic measurements, and allows affinity constants to be determined more straightforwardly.
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Affiliation(s)
- Xiaoying Wang
- College of Chemistry and Chemical Engineering, Central South University , Changsha, Hunan, P. R. China , 410083.,Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
| | - Zhiqiang Li
- College of Chemistry and Chemical Engineering, Central South University , Changsha, Hunan, P. R. China , 410083.,Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
| | - Nguyen Ly
- Biosensing Instrument Inc. , Tempe, Arizona 85284, United States
| | - Feimeng Zhou
- Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
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44
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Kamat V, Rafique A. Exploring sensitivity & throughput of a parallel flow SPRi biosensor for characterization of antibody-antigen interaction. Anal Biochem 2017; 525:8-22. [PMID: 28223164 DOI: 10.1016/j.ab.2017.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/06/2017] [Accepted: 02/14/2017] [Indexed: 12/12/2022]
Abstract
Rapid growth in the field of biotherapeutics has led to an increased demand for high-throughput, label-free biosensors exhibiting high sensitivity. To support the current needs, Sierra Sensors introduced a surface plasmon resonance imaging (SPRi) based biosensor, Molecular Affinity Screening System (MASS-1). We assessed the potential utility of MASS-1 to support Regeneron's therapeutic antibody discovery. A large panel of antibody-antigen interactions was characterized using MASS-1 and the kinetic data were compared with the Biacore 4000 biosensor. Less than 10% deviation in the binding rate constants measured across eight flow channels of MASS-1 was observed. The single injection cycle kinetic assay allowed rapid measurement of binding rate constants for antibody-antigen interactions. MASS-1 sensitivity was independent of protein immobilization level and kinetic analysis performed using ultra-low density mAb surfaces allowed characterization of picomolar affinity interactions without mass transport limitation. High-throughput characterization of a panel of 189 monoclonal antibodies to 13 different antigens with molecular weights ranging from 14kD to 105kD revealed that binding kinetic parameters measured on MASS-1 were comparable to those measured on Biacore 4000. Our data demonstrate that MASS-1 measures reliable binding kinetic parameters and has an appropriate combination of throughput and sensitivity to support discovery and development of therapeutic antibodies.
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Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
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45
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Sun YS, Landry JP, Zhu XD. Evaluation of Kinetics Using Label-Free Optical Biosensors. INSTRUMENTATION SCIENCE & TECHNOLOGY 2017; 45:486-505. [PMID: 30906180 PMCID: PMC6430235 DOI: 10.1080/10739149.2016.1277535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Optical biosensors provide a platform for qualitatively and quantitatively analyzing various biomolecular interactions. In addition to advantages such as label-free and high-throughput detection, these devices are also capable of measuring real-time binding curves in response to changes in optical properties of biomolecules. These kinetic data may be fitted to models to extract binding affinities such as association rates, dissociation rates, and equilibrium dissociation constants. In these biosensors, one of the binding pair is usually immobilized on a solid substrate for capturing the other. Due to the nature of these surface-based methods, mass transport effects and immobilization heterogenetity may cause problems when fitting the kinetic curves with the simple one-to-one Langmuir model. Here real-time binding curves of various antibody-antigen reactions were obtained by using an ellipsometry-based biosensor, and the results were fitted to the simple one-to-one model as well as a more sophisticated approach. The results show that the one-to-two model fitted much better to the curves than the one-to-one model. The two-site model may be explained by assuming two immobilization configurations on the surface. In summary, in fitting real-time curves obtained from optical biosensors, more sophisticated models are usually required to take surface-related issues, such as immobilization heterogenetity and mass transport effects within targets, into account.
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Affiliation(s)
- Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - James P. Landry
- Department of Physics, University of California at Davis, Davis, CA, USA
| | - X. D. Zhu
- Department of Physics, University of California at Davis, Davis, CA, USA
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46
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Kaminski T, Gunnarsson A, Geschwindner S. Harnessing the Versatility of Optical Biosensors for Target-Based Small-Molecule Drug Discovery. ACS Sens 2017; 2:10-15. [PMID: 28722441 DOI: 10.1021/acssensors.6b00735] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Optical biosensors entered target-based small-molecule drug discovery more than two decades ago and have since transformed into a value-adding component in the decision-making process. Here, we briefly highlight the major application areas of optical biosensors and focus on desirable profiles of such platforms in order to ensure their effective use in small molecule drug discovery. Furthermore, we will emphasize current technology-based constraints and discuss experimental strategies to address these limitations as well as provide a view of necessary technology improvements for next generation platforms.
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Affiliation(s)
- Tim Kaminski
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
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47
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Abdiche YN, Yeung AY, Ni I, Stone D, Miles A, Morishige W, Rossi A, Strop P. Antibodies Targeting Closely Adjacent or Minimally Overlapping Epitopes Can Displace One Another. PLoS One 2017; 12:e0169535. [PMID: 28060885 PMCID: PMC5218414 DOI: 10.1371/journal.pone.0169535] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/18/2016] [Indexed: 12/13/2022] Open
Abstract
Here we describe how real-time label-free biosensors can be used to identify antibodies that compete for closely adjacent or minimally overlapping epitopes on their specific antigen via a mechanism of antibody displacement. By kinetically perturbing one another’s binding towards their antigen via the formation of a transient trimolecular complex, antibodies can displace one another in a fully reversible and dose-dependent manner. Displacements can be readily identified when epitope binning assays are performed in a classical sandwich assay format whereby a solution antibody (analyte) is tested for binding to its antigen that is first captured via an immobilized antibody (ligand) because an inverted sandwiching response is observed when an analyte displaces a ligand, signifying the antigen’s unusually rapid dissociation from its ligand. In addition to classifying antibodies within a panel in terms of their ability to block or sandwich pair with one another, displacement provides a hybrid mechanism of competition. Using high-throughput epitope binning studies we demonstrate that displacements can be observed on any target, if the antibody panel contains appropriate epitope diversity. Unidirectional displacements occurring between disparate-affinity antibodies can generate apparent asymmetries in a cross-blocking experiment, confounding their interpretation. However, examining competition across a wide enough concentration range will often reveal that these displacements are reversible. Displacement provides a gentle and efficient way of eluting antigen from an otherwise high affinity binding partner which can be leveraged in designing reagents or therapeutic antibodies with unique properties.
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Affiliation(s)
- Yasmina Noubia Abdiche
- Department of Protein Engineering, Rinat, Oncology Research and Development, Pfizer Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Andy Yik Yeung
- Department of Protein Engineering, Rinat, Oncology Research and Development, Pfizer Inc., South San Francisco, California, United States of America
| | - Irene Ni
- Department of Protein Engineering, Rinat, Oncology Research and Development, Pfizer Inc., South San Francisco, California, United States of America
| | - Donna Stone
- Department of Protein Engineering, Rinat, Oncology Research and Development, Pfizer Inc., South San Francisco, California, United States of America
| | - Adam Miles
- Wasatch Microfluidics, Salt Lake City, Utah, United States of America
| | - Winse Morishige
- Department of Protein Engineering, Bristol-Myers Squibb, Redwood City, California, United States of America
| | - Andrea Rossi
- Compugen USA Inc., South San Francisco, California, United States of America
| | - Pavel Strop
- Department of Protein Engineering, Bristol-Myers Squibb, Redwood City, California, United States of America
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48
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Abstract
The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1514 papers that involved the application of biosensor data were identified for the year 2009 alone (Rich and Myszka, J Mol Recognit 24:892-914, 2011), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay setup while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterization of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilized surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.
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Affiliation(s)
- Paul Leonard
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Stephen Hearty
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Hui Ma
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Richard O'Kennedy
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland.
- School of Biotechnology, Dublin City University, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
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49
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Sun YS, Zhu XD. Real-time, label-free characterization of oligosaccharide-binding proteins using carbohydrate microarrays and an ellipsometry-based biosensor. INSTRUMENTATION SCIENCE & TECHNOLOGY 2017; 45:506-524. [PMID: 30918436 PMCID: PMC6432655 DOI: 10.1080/10739149.2016.1278017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Carbohydrates present on cell surfaces mediate cell behavior through interactions with other biomolecules. Due to their structural complexity, diversity, and heterogeneity, it is difficult to fully characterize a variety of carbohydrates and their binding partners. As a result, novel technologies for glycomics applications have been developed, including carbohydrate microarrays and label-free detection methods. In this paper, we report using the combination of oligosaccharide microarrays and the label-free oblique-incidence reflectivity difference (OI-RD) microscopy for real-time characterization of oligosaccharide binding proteins. Aminated human milk oligosaccharides were immobilized on epoxy-coated glass substrates as microarrays for reactions with Family 1 of solute binding proteins from Bifidobacterium longum subsp. infantis (B. infantis). Binding affinities of these protein-oligosaccharide interactions showed preferences of Family 1 of solute binding proteins to host glycans, which helps in characterizing the complex process of human milk oligosaccharides foraging by B. infantis.
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Affiliation(s)
- Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New
Taipei City, Taiwan
| | - X. D. Zhu
- Department of Physics, University of California at Davis,
Davis, CA, USA
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50
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Lu X, Nicovich PR, Gaus K, Gooding JJ. Towards single molecule biosensors using super-resolution fluorescence microscopy. Biosens Bioelectron 2016; 93:1-8. [PMID: 27829565 DOI: 10.1016/j.bios.2016.10.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/21/2016] [Accepted: 10/20/2016] [Indexed: 11/15/2022]
Abstract
Conventional immunosensors require many binding events to give a single transducer output which represents the concentration of the analyte in the sample. Because of the requirements to selectively detect species in complex samples, immunosensing interfaces must allow immobilisation of antibodies while repelling nonspecific adsorption of other species. These requirements lead to quite sophisticated interfacial design, often with molecular level control, but we have no tools to characterise how well these interfaces work at the molecular level. The work reported herein is an initial feasibility study to show that antibody-antigen binding events can be monitored at the single molecule level using single molecule localisation microscopy (SMLM). The steps to achieve this first requires showing that indium tin oxide surfaces can be used for SMLM, then that these surfaces can be modified with self-assembled monolayers using organophosphonic acid derivatives, that the amount of antigens and antibodies on the surface can be controlled and monitored at the single molecule level and finally antibody binding to antigen modified surfaces can be monitored. The results show the amount of antibody that binds to an antigen modified surface is dependent on both the concentration of antigen on the surface and the concentration of antibody in solution. This study demonstrates the potential of SMLM for characterising biosensing interfaces and as the transducer in a massively parallel, wide field, single molecule detection scheme for quantitative analysis.
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Affiliation(s)
- Xun Lu
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Philip R Nicovich
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia.
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